CASE Model Testing

Obtain the posterior probabilities and estimates of the cis-eQTL effect sizes.

CASE_test(
  Z = NULL,
  R,
  hatB = NULL,
  hatS = NULL,
  N,
  CASE_training,
  verbose = TRUE,
  ...
)

Arguments

Z

M * C matrix of z scores.

R

M * M matrix of LD.

hatB

M * C matrix of the estimated effects. Alternative summary data (together with hatS) to be provided instead of Z.

hatS

M * C matrix of standard errors of the estimated effects. Alternative summary data (together with hatB) to be provided instead of Z.

N

either 1 or C vector of the sample size, or C * C matrix of the sample size (diagonal) and overlaps (off-diagonal). If provided with a vector, CASE assumes that each pair of traits overlaps with their minimal sample size.

CASE_training

A "CASE_training" object.

verbose

(optional) logical, whether to print logging information. Default = TRUE.

...

additional arguments.

Value

A "CASE" object with the following elements:

pi:

L-vector, the prior probabilities of sharing patterns.

U:

L-list of C * C matrix, the prior covariances of sharing patterns.

V:

C * C matrix, the sample-adjusted phenotypical variance.

pip:

M * C matrix, posterior probability of having eQTL effects per SNP per cell type.

post_mean:

M * C matrix, average posterior estimates of eQTL effects per SNP per cell type.

Details

TBD

References

TBD

Author

Chen Lin, Hongyu Zhao